Hello, I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 3.2.3, including dplyr package. I am unable to successfully install it. Below I show the failed installation using utils::install.packages() and then again using devtools::install_github(). Each yields an error similar to the other but not quite exactly the same - the error messages sail right over my head. I can contact the package author if that would be better, but thought it best to start here. Thanks! Ben Ben Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org> sessionInfo()R version 3.2.3 (2015-12-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.7 (Final) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base #### # utils::install.packages() ####> install.packages("dplyr", repo = "http://cran.r-project.org")Installing package into ?/usr/lib64/R/library? (as ?lib? is unspecified) trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz' Content type 'application/x-gzip' length 655997 bytes (640 KB) =================================================downloaded 640 KB * installing *source* package ?dplyr? ... ** package ?dplyr? successfully unpacked and MD5 sums checked ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o In file included from ../inst/include/dplyr.h:131, from arrange.cpp:1: ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ?column? may be used uninitialized in this function g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: dplyr.cpp:242: warning: ?number_tiles? may be used uninitialized in this function {standard input}: Assembler messages: {standard input}:509159: Warning: end of file not at end of a line; newline inserted {standard input}:509591: Error: open CFI at the end of file; missing .cfi_endproc directive g++: Internal error: Killed (program cc1plus) Please submit a full bug report. See <http://bugzilla.redhat.com/bugzilla> for instructions. make: *** [dplyr.o] Error 1 ERROR: compilation failed for package ?dplyr? * removing ?/usr/lib64/R/library/dplyr? The downloaded source packages are in ?/tmp/RtmpkdCODF/downloaded_packages? Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("dplyr", repo = "http://cran.r-project.org") : installation of package ?dplyr? had non-zero exit status #### # devtools::install_github() ####> library(devtools) > install_github("hadley/dplyr", lib = '/usr/lib64/R/library')Using GitHub PAT from envvar GITHUB_PAT Downloading GitHub repo hadley/dplyr at master from URL https://api.github.com/repos/hadley/dplyr/zipball/master Installing dplyr Using GitHub PAT from envvar GITHUB_PAT Downloading GitHub repo hadley/testthat at master from URL https://api.github.com/repos/hadley/testthat/zipball/master Installing testthat '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL \ '/tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494' \ --library='/usr/lib64/R/library' --install-tests * installing *source* package ?testthat? ... ** libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c label.c -o label.o gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c reassign.c -o reassign.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-catch.cpp -o test-catch.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-example.cpp -o test-example.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-runner.cpp -o test-runner.o g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib64/R/lib -lR installing to /usr/lib64/R/library/testthat/libs ** R ** inst ** tests ** preparing package for lazy loading ** help *** installing help indices converting help for package ?testthat? finding HTML links ... done CheckReporter html FailReporter html ListReporter html MinimalReporter html MultiReporter html Reporter html RstudioReporter html SilentReporter html StopReporter html SummaryReporter html TapReporter html TeamcityReporter html auto_test html auto_test_package html compare html compare_state html comparison-expectations html context html describe html dir_state html equality-expectations html evaluate_promise html expect_cpp_tests_pass html expect_equal_to_reference html expect_length html expect_match html expect_named html expect_success html expect_that html expectation html fail html find_reporter html find_test_scripts html inheritance-expectations html logical-expectations html make_expectation html not html oldskool html output-expectations html reexports html Rd warning: /tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494/man/reexports.Rd:13: missing file link ?%>%? reporter-accessors html safe_digest html skip html source_file html takes_less_than html test_dir html test_env html test_examples html test_file html test_package html test_path html test_that html testthat html testthat_results html try_again html use_catch html watch html with_mock html ** building package indices ** testing if installed package can be loaded * DONE (testthat) Making 'packages.html' ... done Using GitHub PAT from envvar GITHUB_PAT Skipping install for github remote, the SHA1 (cb38672f) has not changed since last install. Use `force = TRUE` to force installation Skipping 2 packages ahead of CRAN: lazyeval, tibble '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL \ '/tmp/RtmpkdCODF/devtools45c2fff716f/hadley-dplyr-afb9ac7' \ --library='/usr/lib64/R/library' --install-tests * installing *source* package ?dplyr? ... ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o In file included from ../inst/include/dplyr.h:141, from arrange.cpp:1: ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: dplyr.cpp:213: warning: ?number_tiles? may be used uninitialized in this function In file included from ../inst/include/dplyr.h:141, from dplyr.cpp:1: ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function {standard input}: Assembler messages: {standard input}:812569: Warning: end of file not at end of a line; newline inserted g++: Internal error: Killed (program cc1plus) Please submit a full bug report. See <http://bugzilla.redhat.com/bugzilla> for instructions. make: *** [dplyr.o] Error 1 ERROR: compilation failed for package ?dplyr? * removing ?/usr/lib64/R/library/dplyr? Error: Command failed (1)>
You normally see these errors when compiling on a vm that has very little memory. Hadley On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper <btupper at bigelow.org> wrote:> Hello, > > I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 3.2.3, including dplyr package. I am unable to successfully install it. Below I show the failed installation using utils::install.packages() and then again using devtools::install_github(). Each yields an error similar to the other but not quite exactly the same - the error messages sail right over my head. > > I can contact the package author if that would be better, but thought it best to start here. > > Thanks! > Ben > > Ben Tupper > Bigelow Laboratory for Ocean Sciences > 60 Bigelow Drive, P.O. Box 380 > East Boothbay, Maine 04544 > http://www.bigelow.org > >> sessionInfo() > R version 3.2.3 (2015-12-10) > Platform: x86_64-redhat-linux-gnu (64-bit) > Running under: CentOS release 6.7 (Final) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > > #### > # utils::install.packages() > #### > >> install.packages("dplyr", repo = "http://cran.r-project.org") > Installing package into ?/usr/lib64/R/library? > (as ?lib? is unspecified) > trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz' > Content type 'application/x-gzip' length 655997 bytes (640 KB) > =================================================> downloaded 640 KB > > * installing *source* package ?dplyr? ... > ** package ?dplyr? successfully unpacked and MD5 sums checked > ** libs > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o > In file included from ../inst/include/dplyr.h:131, > from arrange.cpp:1: > ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: > ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ?column? may be used uninitialized in this function > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o > dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: > dplyr.cpp:242: warning: ?number_tiles? may be used uninitialized in this function > {standard input}: Assembler messages: > {standard input}:509159: Warning: end of file not at end of a line; newline inserted > {standard input}:509591: Error: open CFI at the end of file; missing .cfi_endproc directive > g++: Internal error: Killed (program cc1plus) > Please submit a full bug report. > See <http://bugzilla.redhat.com/bugzilla> for instructions. > make: *** [dplyr.o] Error 1 > ERROR: compilation failed for package ?dplyr? > * removing ?/usr/lib64/R/library/dplyr? > > The downloaded source packages are in > ?/tmp/RtmpkdCODF/downloaded_packages? > Updating HTML index of packages in '.Library' > Making 'packages.html' ... done > Warning message: > In install.packages("dplyr", repo = "http://cran.r-project.org") : > installation of package ?dplyr? had non-zero exit status > > > > #### > # devtools::install_github() > #### > > >> library(devtools) >> install_github("hadley/dplyr", lib = '/usr/lib64/R/library') > Using GitHub PAT from envvar GITHUB_PAT > Downloading GitHub repo hadley/dplyr at master > from URL https://api.github.com/repos/hadley/dplyr/zipball/master > Installing dplyr > Using GitHub PAT from envvar GITHUB_PAT > Downloading GitHub repo hadley/testthat at master > from URL https://api.github.com/repos/hadley/testthat/zipball/master > Installing testthat > '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ > --quiet CMD INSTALL \ > '/tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494' \ > --library='/usr/lib64/R/library' --install-tests > > * installing *source* package ?testthat? ... > ** libs > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c label.c -o label.o > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c reassign.c -o reassign.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-catch.cpp -o test-catch.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-example.cpp -o test-example.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-runner.cpp -o test-runner.o > g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib64/R/lib -lR > installing to /usr/lib64/R/library/testthat/libs > ** R > ** inst > ** tests > ** preparing package for lazy loading > ** help > *** installing help indices > converting help for package ?testthat? > finding HTML links ... done > CheckReporter html > FailReporter html > ListReporter html > MinimalReporter html > MultiReporter html > Reporter html > RstudioReporter html > SilentReporter html > StopReporter html > SummaryReporter html > TapReporter html > TeamcityReporter html > auto_test html > auto_test_package html > compare html > compare_state html > comparison-expectations html > context html > describe html > dir_state html > equality-expectations html > evaluate_promise html > expect_cpp_tests_pass html > expect_equal_to_reference html > expect_length html > expect_match html > expect_named html > expect_success html > expect_that html > expectation html > fail html > find_reporter html > find_test_scripts html > inheritance-expectations html > logical-expectations html > make_expectation html > not html > oldskool html > output-expectations html > reexports html > Rd warning: /tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494/man/reexports.Rd:13: missing file link ?%>%? > reporter-accessors html > safe_digest html > skip html > source_file html > takes_less_than html > test_dir html > test_env html > test_examples html > test_file html > test_package html > test_path html > test_that html > testthat html > testthat_results html > try_again html > use_catch html > watch html > with_mock html > ** building package indices > ** testing if installed package can be loaded > * DONE (testthat) > Making 'packages.html' ... done > Using GitHub PAT from envvar GITHUB_PAT > Skipping install for github remote, the SHA1 (cb38672f) has not changed since last install. > Use `force = TRUE` to force installation > Skipping 2 packages ahead of CRAN: lazyeval, tibble > '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ > --quiet CMD INSTALL \ > '/tmp/RtmpkdCODF/devtools45c2fff716f/hadley-dplyr-afb9ac7' \ > --library='/usr/lib64/R/library' --install-tests > > * installing *source* package ?dplyr? ... > ** libs > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o > In file included from ../inst/include/dplyr.h:141, > from arrange.cpp:1: > ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: > ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o > dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: > dplyr.cpp:213: warning: ?number_tiles? may be used uninitialized in this function > In file included from ../inst/include/dplyr.h:141, > from dplyr.cpp:1: > ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: > ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function > {standard input}: Assembler messages: > {standard input}:812569: Warning: end of file not at end of a line; newline inserted > g++: Internal error: Killed (program cc1plus) > Please submit a full bug report. > See <http://bugzilla.redhat.com/bugzilla> for instructions. > make: *** [dplyr.o] Error 1 > ERROR: compilation failed for package ?dplyr? > * removing ?/usr/lib64/R/library/dplyr? > Error: Command failed (1) >> > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- http://hadley.nz
Hi, OK - that can be fixed by our IT whizzes. Thanks, Ben P.S. Thanks for dplyr!> On Apr 19, 2016, at 4:10 PM, Hadley Wickham <h.wickham at gmail.com> wrote: > > You normally see these errors when compiling on a vm that has very > little memory. > Hadley > > On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper <btupper at bigelow.org> wrote: >> Hello, >> >> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 3.2.3, including dplyr package. I am unable to successfully install it. Below I show the failed installation using utils::install.packages() and then again using devtools::install_github(). Each yields an error similar to the other but not quite exactly the same - the error messages sail right over my head. >> >> I can contact the package author if that would be better, but thought it best to start here. >> >> Thanks! >> Ben >> >> Ben Tupper >> Bigelow Laboratory for Ocean Sciences >> 60 Bigelow Drive, P.O. Box 380 >> East Boothbay, Maine 04544 >> http://www.bigelow.org >> >>> sessionInfo() >> R version 3.2.3 (2015-12-10) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> Running under: CentOS release 6.7 (Final) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> >> #### >> # utils::install.packages() >> #### >> >>> install.packages("dplyr", repo = "http://cran.r-project.org") >> Installing package into ?/usr/lib64/R/library? >> (as ?lib? is unspecified) >> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz' >> Content type 'application/x-gzip' length 655997 bytes (640 KB) >> =================================================>> downloaded 640 KB >> >> * installing *source* package ?dplyr? ... >> ** package ?dplyr? successfully unpacked and MD5 sums checked >> ** libs >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o >> In file included from ../inst/include/dplyr.h:131, >> from arrange.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ?column? may be used uninitialized in this function >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o >> dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: >> dplyr.cpp:242: warning: ?number_tiles? may be used uninitialized in this function >> {standard input}: Assembler messages: >> {standard input}:509159: Warning: end of file not at end of a line; newline inserted >> {standard input}:509591: Error: open CFI at the end of file; missing .cfi_endproc directive >> g++: Internal error: Killed (program cc1plus) >> Please submit a full bug report. >> See <http://bugzilla.redhat.com/bugzilla> for instructions. >> make: *** [dplyr.o] Error 1 >> ERROR: compilation failed for package ?dplyr? >> * removing ?/usr/lib64/R/library/dplyr? >> >> The downloaded source packages are in >> ?/tmp/RtmpkdCODF/downloaded_packages? >> Updating HTML index of packages in '.Library' >> Making 'packages.html' ... done >> Warning message: >> In install.packages("dplyr", repo = "http://cran.r-project.org") : >> installation of package ?dplyr? had non-zero exit status >> >> >> >> #### >> # devtools::install_github() >> #### >> >> >>> library(devtools) >>> install_github("hadley/dplyr", lib = '/usr/lib64/R/library') >> Using GitHub PAT from envvar GITHUB_PAT >> Downloading GitHub repo hadley/dplyr at master >> from URL https://api.github.com/repos/hadley/dplyr/zipball/master >> Installing dplyr >> Using GitHub PAT from envvar GITHUB_PAT >> Downloading GitHub repo hadley/testthat at master >> from URL https://api.github.com/repos/hadley/testthat/zipball/master >> Installing testthat >> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ >> --quiet CMD INSTALL \ >> '/tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494' \ >> --library='/usr/lib64/R/library' --install-tests >> >> * installing *source* package ?testthat? ... >> ** libs >> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c label.c -o label.o >> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c reassign.c -o reassign.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-catch.cpp -o test-catch.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-example.cpp -o test-example.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-runner.cpp -o test-runner.o >> g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib64/R/lib -lR >> installing to /usr/lib64/R/library/testthat/libs >> ** R >> ** inst >> ** tests >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> converting help for package ?testthat? >> finding HTML links ... done >> CheckReporter html >> FailReporter html >> ListReporter html >> MinimalReporter html >> MultiReporter html >> Reporter html >> RstudioReporter html >> SilentReporter html >> StopReporter html >> SummaryReporter html >> TapReporter html >> TeamcityReporter html >> auto_test html >> auto_test_package html >> compare html >> compare_state html >> comparison-expectations html >> context html >> describe html >> dir_state html >> equality-expectations html >> evaluate_promise html >> expect_cpp_tests_pass html >> expect_equal_to_reference html >> expect_length html >> expect_match html >> expect_named html >> expect_success html >> expect_that html >> expectation html >> fail html >> find_reporter html >> find_test_scripts html >> inheritance-expectations html >> logical-expectations html >> make_expectation html >> not html >> oldskool html >> output-expectations html >> reexports html >> Rd warning: /tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494/man/reexports.Rd:13: missing file link ?%>%? >> reporter-accessors html >> safe_digest html >> skip html >> source_file html >> takes_less_than html >> test_dir html >> test_env html >> test_examples html >> test_file html >> test_package html >> test_path html >> test_that html >> testthat html >> testthat_results html >> try_again html >> use_catch html >> watch html >> with_mock html >> ** building package indices >> ** testing if installed package can be loaded >> * DONE (testthat) >> Making 'packages.html' ... done >> Using GitHub PAT from envvar GITHUB_PAT >> Skipping install for github remote, the SHA1 (cb38672f) has not changed since last install. >> Use `force = TRUE` to force installation >> Skipping 2 packages ahead of CRAN: lazyeval, tibble >> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ >> --quiet CMD INSTALL \ >> '/tmp/RtmpkdCODF/devtools45c2fff716f/hadley-dplyr-afb9ac7' \ >> --library='/usr/lib64/R/library' --install-tests >> >> * installing *source* package ?dplyr? ... >> ** libs >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o >> In file included from ../inst/include/dplyr.h:141, >> from arrange.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o >> dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: >> dplyr.cpp:213: warning: ?number_tiles? may be used uninitialized in this function >> In file included from ../inst/include/dplyr.h:141, >> from dplyr.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function >> {standard input}: Assembler messages: >> {standard input}:812569: Warning: end of file not at end of a line; newline inserted >> g++: Internal error: Killed (program cc1plus) >> Please submit a full bug report. >> See <http://bugzilla.redhat.com/bugzilla> for instructions. >> make: *** [dplyr.o] Error 1 >> ERROR: compilation failed for package ?dplyr? >> * removing ?/usr/lib64/R/library/dplyr? >> Error: Command failed (1) >>> >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > > -- > http://hadley.nzBen Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org
Increasing memory resolved the issue for me. Thanks again, Ben> On Apr 19, 2016, at 4:10 PM, Hadley Wickham <h.wickham at gmail.com> wrote: > > You normally see these errors when compiling on a vm that has very > little memory. > Hadley > > On Tue, Apr 19, 2016 at 2:47 PM, Ben Tupper <btupper at bigelow.org> wrote: >> Hello, >> >> I am getting a fresh CentOS 6.7 machine set up with all of the goodies for R 3.2.3, including dplyr package. I am unable to successfully install it. Below I show the failed installation using utils::install.packages() and then again using devtools::install_github(). Each yields an error similar to the other but not quite exactly the same - the error messages sail right over my head. >> >> I can contact the package author if that would be better, but thought it best to start here. >> >> Thanks! >> Ben >> >> Ben Tupper >> Bigelow Laboratory for Ocean Sciences >> 60 Bigelow Drive, P.O. Box 380 >> East Boothbay, Maine 04544 >> http://www.bigelow.org >> >>> sessionInfo() >> R version 3.2.3 (2015-12-10) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> Running under: CentOS release 6.7 (Final) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> >> #### >> # utils::install.packages() >> #### >> >>> install.packages("dplyr", repo = "http://cran.r-project.org") >> Installing package into ?/usr/lib64/R/library? >> (as ?lib? is unspecified) >> trying URL 'http://cran.r-project.org/src/contrib/dplyr_0.4.3.tar.gz' >> Content type 'application/x-gzip' length 655997 bytes (640 KB) >> =================================================>> downloaded 640 KB >> >> * installing *source* package ?dplyr? ... >> ** package ?dplyr? successfully unpacked and MD5 sums checked >> ** libs >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o >> In file included from ../inst/include/dplyr.h:131, >> from arrange.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:40: warning: ?column? may be used uninitialized in this function >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o >> dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: >> dplyr.cpp:242: warning: ?number_tiles? may be used uninitialized in this function >> {standard input}: Assembler messages: >> {standard input}:509159: Warning: end of file not at end of a line; newline inserted >> {standard input}:509591: Error: open CFI at the end of file; missing .cfi_endproc directive >> g++: Internal error: Killed (program cc1plus) >> Please submit a full bug report. >> See <http://bugzilla.redhat.com/bugzilla> for instructions. >> make: *** [dplyr.o] Error 1 >> ERROR: compilation failed for package ?dplyr? >> * removing ?/usr/lib64/R/library/dplyr? >> >> The downloaded source packages are in >> ?/tmp/RtmpkdCODF/downloaded_packages? >> Updating HTML index of packages in '.Library' >> Making 'packages.html' ... done >> Warning message: >> In install.packages("dplyr", repo = "http://cran.r-project.org") : >> installation of package ?dplyr? had non-zero exit status >> >> >> >> #### >> # devtools::install_github() >> #### >> >> >>> library(devtools) >>> install_github("hadley/dplyr", lib = '/usr/lib64/R/library') >> Using GitHub PAT from envvar GITHUB_PAT >> Downloading GitHub repo hadley/dplyr at master >> from URL https://api.github.com/repos/hadley/dplyr/zipball/master >> Installing dplyr >> Using GitHub PAT from envvar GITHUB_PAT >> Downloading GitHub repo hadley/testthat at master >> from URL https://api.github.com/repos/hadley/testthat/zipball/master >> Installing testthat >> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ >> --quiet CMD INSTALL \ >> '/tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494' \ >> --library='/usr/lib64/R/library' --install-tests >> >> * installing *source* package ?testthat? ... >> ** libs >> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c label.c -o label.o >> gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c reassign.c -o reassign.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-catch.cpp -o test-catch.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-example.cpp -o test-example.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c test-runner.cpp -o test-runner.o >> g++ -m64 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o testthat.so label.o reassign.o test-catch.o test-example.o test-runner.o -L/usr/lib64/R/lib -lR >> installing to /usr/lib64/R/library/testthat/libs >> ** R >> ** inst >> ** tests >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> converting help for package ?testthat? >> finding HTML links ... done >> CheckReporter html >> FailReporter html >> ListReporter html >> MinimalReporter html >> MultiReporter html >> Reporter html >> RstudioReporter html >> SilentReporter html >> StopReporter html >> SummaryReporter html >> TapReporter html >> TeamcityReporter html >> auto_test html >> auto_test_package html >> compare html >> compare_state html >> comparison-expectations html >> context html >> describe html >> dir_state html >> equality-expectations html >> evaluate_promise html >> expect_cpp_tests_pass html >> expect_equal_to_reference html >> expect_length html >> expect_match html >> expect_named html >> expect_success html >> expect_that html >> expectation html >> fail html >> find_reporter html >> find_test_scripts html >> inheritance-expectations html >> logical-expectations html >> make_expectation html >> not html >> oldskool html >> output-expectations html >> reexports html >> Rd warning: /tmp/RtmpkdCODF/devtools45c22638b2f2/hadley-testthat-52d5494/man/reexports.Rd:13: missing file link ?%>%? >> reporter-accessors html >> safe_digest html >> skip html >> source_file html >> takes_less_than html >> test_dir html >> test_env html >> test_examples html >> test_file html >> test_package html >> test_path html >> test_that html >> testthat html >> testthat_results html >> try_again html >> use_catch html >> watch html >> with_mock html >> ** building package indices >> ** testing if installed package can be loaded >> * DONE (testthat) >> Making 'packages.html' ... done >> Using GitHub PAT from envvar GITHUB_PAT >> Skipping install for github remote, the SHA1 (cb38672f) has not changed since last install. >> Use `force = TRUE` to force installation >> Skipping 2 packages ahead of CRAN: lazyeval, tibble >> '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ >> --quiet CMD INSTALL \ >> '/tmp/RtmpkdCODF/devtools45c2fff716f/hadley-dplyr-afb9ac7' \ >> --library='/usr/lib64/R/library' --install-tests >> >> * installing *source* package ?dplyr? ... >> ** libs >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c address.cpp -o address.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c api.cpp -o api.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c arrange.cpp -o arrange.o >> In file included from ../inst/include/dplyr.h:141, >> from arrange.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c between.cpp -o between.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c bind.cpp -o bind.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c combine_variables.cpp -o combine_variables.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c distinct.cpp -o distinct.o >> g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -DBOOST_NO_INT64_T -DBOOST_NO_INTEGRAL_INT64_T -DBOOST_NO_LONG_LONG -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c dplyr.cpp -o dplyr.o >> dplyr.cpp: In function ?dplyr::Result* ntile_prototype(SEXPREC*, const dplyr::LazySubsets&, int)?: >> dplyr.cpp:213: warning: ?number_tiles? may be used uninitialized in this function >> In file included from ../inst/include/dplyr.h:141, >> from dplyr.cpp:1: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h: In constructor ?dplyr::DataFrameSubsetVisitors::DataFrameSubsetVisitors(const Rcpp::DataFrame&, const Rcpp::CharacterVector&)?: >> ../inst/include/dplyr/DataFrameSubsetVisitors.h:41: warning: ?column? may be used uninitialized in this function >> {standard input}: Assembler messages: >> {standard input}:812569: Warning: end of file not at end of a line; newline inserted >> g++: Internal error: Killed (program cc1plus) >> Please submit a full bug report. >> See <http://bugzilla.redhat.com/bugzilla> for instructions. >> make: *** [dplyr.o] Error 1 >> ERROR: compilation failed for package ?dplyr? >> * removing ?/usr/lib64/R/library/dplyr? >> Error: Command failed (1) >>> >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > > -- > http://hadley.nzBen Tupper Bigelow Laboratory for Ocean Sciences 60 Bigelow Drive, P.O. Box 380 East Boothbay, Maine 04544 http://www.bigelow.org
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